title: RNA sequencing of clr4[delta] cells


title: C1_TGF-β1_0h

status: Public on Nov 29 2019

type: RNA

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with R with RMA normalization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: dermal fibroblasts

label_protocol: Standard Affymetrix protocol

growth_protocol: Dermal fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol: Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN

treatment_protocol: Cells were left untreated or treated for 2, 6, or 24 hours with TGF-β1 (10 ng/ml)

tag: cell type

value: dermal fibroblasts

tag: disease state

value: healthy control

tag: mutation

tag: treatment

value: untreated


title: D73

status: Public on Nov 28 2019

type: genomic

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Samples were hybridized onto Affymetrix OncoScan FFPE Assay kit arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery 9.0 edition Software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

molecule: genomic DNA

source_name: Tonsil

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

value: Diffuse large B-cell lymphoma

tag: gender

value: Male

tag: tissue

value: FFPE


title: D71

source_name: Intestinal mucosa


title: D42

source_name: LN mediastinum


title: D65

hyb_protocol: Samples were hybridized onto  Affymetrix OncoScan FFPE Assay ki arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

source_name: Retroperitoneal mass

value: High grade B-cell lymphoma, NOS


title: D69

source_name: Intestine

value: Large B-cell lymphopma with IRF4 rearrangement


title: Control2-IL-17A_24h

type: SRA

library_source: transcriptomic

data_processing:
Sequence reads were aligned using STAR aligner with GRCh37 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

source_name: skin fibroblasts

growth_protocol: Skin fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were left untreated or treated for 2, 6, or 24 hours with IL-17A (100 ng/ml) or TGF-β1 (10 ng/ml)

value: skin fibroblasts

value: control

tag: time point


title: D70

source_name: Axilar lymph node


title: D64

source_name: Inguinal lymph node


title: Tim4p_naive_b1_4

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.

organism: Mus musculus

label_protocol: 20 ng of RNA from each sample was used to synthesize biotinylated probes,  according to a double amplification protocol using MessageAmpTM II aRNA Amplification Kit (Ambion).

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol. The lineage cocktail used was a combination of antibodies against CD19 (B cells), T cell receptor beta chain (alpha/beta T cells and NK T cells), NK1.1 (NK and NK T cells) and Ly6G (neutrophiles).

treatment_protocol: To evaluate the impact of the tumor-microenvironment on PM phenotype, we performed global gene expression analysis using microarrays on bulk PM from naïve mice and at different time points (4, 6 or 8 weeks) during ID8 tumor progression.

value: peritoneal cavity

value: macrophage

tag: phenotype

tag: time (in weeks)

tag: strain

value: naive


title: Tim4p_naive_b1_3


title: H_2

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

description:
geneCounts_hg19_H.txt
DESeq_hg19_HT_vs_H.csv

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the T. rubrum and hg19 genomes using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.5 (upregulation) or < -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome and hg19 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

source_name: HaCat cell line, replicate II

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar  for 15 days at 28ºC. Keratinocytes were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and HaCat cell were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: Pre-cultured conidia of T. rubrum were added to HaCat cell line and the co-culture was incubated for 24 h  at 37ºC in a humidified atmosphere containing 5% CO2. To evaluate the effect of terbinafine, 0.0162 µM of the antifungal agent was added to the co-culture

tag: cell line

value: HaCat


title: HT_3

description:
geneCounts_hg19_HT.txt
DESeq_hg19_HT_vs_H.csv

source_name: HaCat cell line treated with terbinafine, replicate III

value: terbinafine


title: H_3

source_name: HaCat cell line, replicate III


title: HT_2

source_name: HaCat cell line treated with terbinafine, replicate II


title: D61


title: D57

source_name: Abdominal mass


title: Rep_virus_3_c_GEN00105093

city: Boston

first: Pierce

last: Ogden

state: MA

address: 3 Blackfan Circle, CLSB 528/4C

country: USA

institute: Harvard

description: sequencing of AAV genome to determine packaing effeciency

library_source: genomic

data_processing:
Library strategy: amplicon seq
for all samples, we use python to process fastqs and counted the  barcodes
the counted barcodes are then merged onto a table containing the allele information for each barcode using python scripts
Genome_build: AAV2
Supplementary_files_format_and_content: barcode abundances and associated mutation information

organism: Adeno-associated virus

source_name: AAV Capsid

extract_protocol:
AAV were isolated according to methods described in paper
libraries were prepared using illumina sequencing primers

tag: experiment

value: capsid packaging screen

value: AAV genome DNA


title: Tim4p_naive_b1_2


title: Tim4p_ID8_8w_b6_4

value: Intra-peritoneal tumor


title: Tim4p_naive_b1_1


title: D55_R

source_name: Left inguinal lymph node


title: Tim4p_ID8_8w_b6_2


title: Tim4p_ID8_8w_b6_3


title: D55


title: Tim4p_ID8_8w_b6_1


title: D54

source_name: Right neck mass

value: Female


title: 44k K562 replication timing

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

description: Nascent DNA

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray or 8 X44K human microarray.

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

source_name: nascent DNA from early S-phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipitated DNA, whole genome amplification (WGA) was conducted (Seq-plex, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells grown in culture condition defined by ATCC.

extract_protocol: Cells were incubated with BrdU (50µM) for two hours, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNase (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipitated by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580). To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

tag: phase

value: Early S-phase

source_name: nascent DNA from late S-phase

value: Late S-phase


title: Tim4p_ID8_6w_b5_4


title: dTG_placenta_small_embryo_2

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

description:
dTG_S2
Gene expression in transgenic placenta with small size embryo, sample 2

hyb_protocol: Labeled cRNA samples were and hybridized to Agilent SurePrint G3 Mouse GE 8x60K microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned on the Agilent DNA Microarray Scanner (G2505B)

data_processing: Raw microarray data were acquired using an Agilent microarray scanner and processed with Agilent Extraction Image Analysis software. After normalizing the samples by quantile normalization and log2 -transformed intensities, we applied the empirical Bayesian algorithm, implemented in the R package “limma” to identify genes that were differentially expressed between normal and transgenic mouse placentas. Benjamini and Hochberg’s method was used to calculate the adjusted p-values to control for false discovery rate.

source_name: placenta Transgenic, small size embryo

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions. Amplified cRNA samples were purified on Qiagen’s RNeasy mini spin columns

extract_protocol: Mouse placentas were collected immediately after euthanasia and washed in PBS then placed in RNA later solution. Each placenta was homogenized using a T10 Basic ULTRA-TURRAX disperser (IKA, Wilmington, NC) in 1 ml of QIAzol lysis reagent (Qiagen, Valencia, CA). Total RNAs were further purified using RNAeasy Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Gene expression profiles were analyzed in placentas from WT mice and transgenic (dTG) mice.

tag: strain background

tag: genotype/variation

value: Transgenic

value: Placenta


title: dTG_placenta_small_embryo_1

description:
dTG_S1
Gene expression in transgenic placenta with small size embryo, sample 1


title: dTG_placenta_small_embryo_3

description:
dTG_3
Gene expression in transgenic placenta with small size embryo, sample 3


title: D53

source_name: Stomach

value: High grade B-cell lymphoma, NOS

value: FFPE


title: dTG_placenta_normal_embryo_3

description:
dTG_N3
Gene expression in transgenic placenta with normal size embryo, sample 3

source_name: placenta Transgenic, normal size embryo


title: dTG_placenta_normal_embryo_1

description:
dTG_N1
Gene expression in transgenic placenta with normal size embryo, sample 1


title: dTG_placenta_normal_embryo_2

description:
dTG_N2
Gene expression in transgenic placenta with normal size embryo, sample 2


title: D52

source_name: Breast


title: Tim4p_ID8_6w_b5_2


title: RNA-seq Mutant3-A187

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Deseq_normalized_gene_expression_with_annotations.txt

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2018_1 were also provide

source_name: sciatic nerve

extract_protocol:
Total RNAs of sciatic nerves were isolated using the RNeasy Kit (Qiagen) including a DNAse treatment step. RNA quality was assessed using RNA Screen Tape 6000 Pico LabChips with the Tape Station (Agilent Technologies) and the RNA concentration was measured by spectrophometry using Xpose.
RNA-seq libraries were prepared starting from 60 ng of total RNA using the Universal Plus mRNA-Seq (Nugen) as recommended by the manufacturer. The oriented cDNA produced from the poly-A+ fraction were PCR amplified (15 cycles).
An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina HiSeq2500 (paired-end reads 130 bases + 130 bases). A mean of 124 millions of passing filter paired-end reads was produced per library sample (with a minimum of 103 million and a maximum 158 millions).

value: sciatic nerve

tag: Stage

value: post-natal day 4

tag: genotype

value: Ht-PA-Cre; Adar1fl/fl;R26R


title: Tim4p_ID8_6w_b5_1

tag: cell type

value: macrophage


title: WT_placenta_normal_embryo_2

description:
WT_N2
Gene expression wild type placenta

source_name: placenta wild type

value: Wild type


title: WT_placenta_normal_embryo_1

description:
WT_N1
Gene expression wild type placenta


title: RNA-seq Control3-A188

value: wild-type


title: RNA-seq Mutant2-A185


title: D51

source_name: Tonsil

value: Large B-cell lymphopma with IRF4 rearrangement


title: RNA-seq Control2-A186


title: RNA-seq Mutant1-A183


title: Tim4p_ID8_4w_b4_4


title: Tim4p_ID8_4w_b4_3


title: D50

source_name: Left cervical lymph node


title: RNA-seq Control1-A184


title: D49_R

value: Male


title: JONAS_2096: Non-transgenic IgG control sample

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

data_processing:
Base-calling was performed by Illumina Real-Time Analysis software v1.17
Reads were aligned by bowtie2 v2.0.5 using only the first 65 bases against the Arabidopsis thaliana TAIR10 reference genome.
Shiftsize was calculated using phantompeakqualtools and default parameters
Peaks called with MACS2 version 2.0.10 with parameters "callpeak -c --format=SAM --gsize=1.19e8 -p 99e-2 --nomodel --shiftsize=[from phantompeakqualtools] --down-sample --call-summits". A concatenated file of all non-transgenic control IP reads was used as the control in peak calling
Genome_build: TAIR10
Supplementary_files_format_and_content: Summit region output created by MACS2 in bed format.

organism: Arabidopsis thaliana

source_name: Three day old etiolated seedlings

growth_protocol: Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.

extract_protocol:
Conducted as described in O'Malley et al. 2016 (doi: 10.1016/j.cell.2016.04.038) and Chang et al. 2013 (10.7554/eLife.00675). Harvested seedlings were crosslinked with 1% formaldehyde under vacuum for 20 minutes then snap-frozen in liquid nitrogen. Nuclei were extracted from frozen, ground seedlings according to Qiao et al. 2016 (10.1126/science.1225974) then sonicated according to Chang et al .2016 using a Diagenode bioruptor to yield an average DNA fragment size of approximately 150-300 bases. Transcription-factor DNA complexes were isolated by immunoprecipitation with polyclonal anti-GFP raised in goat from David Dreschel (Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany) or, for non-transgenic controls, IgG from goat (supplied by Covance). These complexes were then retrieved using Protein G Dynabeads (Life Technologies).
Conducted as described in Chang et al. 2013 (10.7554/eLife.00675) with one modification. Size selection was performed on SPRI beads, instead of on gels, with upper and lower cut-offs to yield a fragment size-range of 150-500 nucleotides. Sequencing was conducted on the Illumina HiSeq 2500 platform.

treatment_protocol: Not treated

value: seedlings

value: Air 2h

tag: chip antibody

value: Goat IgG whole molecule

tag: epitope fusion tag


title: Tim4p_ID8_6w_b5_3

value: Intra-peritoneal tumor

tag: treatment


title: JONAS_2093: Non-transgenic IgG control sample


title: D49

tag: gender


title: D48

source_name: Right tonsil

value: Female

tag: tissue


title: Tim4p_ID8_4w_b4_2


title: HAL_1205: Non-transgenic IgG control sample


title: D47


title: Genomic DNA from BLaER1 at 168h

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 168 hours

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

source_name: RCH-ACV derived cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: time point

value: at 168h

value: RCH-ACV derived cell line


title: MYC3 ChIP-seq rep1

treatment_protocol: Jasmonate treatment was via the gaseous phase. The JA treatment was conducted in a closed container with a concentration of 1 μL methyl jasmonate (95% purity; Sigma-Aldrich) per 1 liter of container volume.

value: JA 2h

value: Polyclonal anti-GFP

value: YpET


title: Tim4n_naive_b1_4

value: peritoneal cavity

tag: phenotype

value: naive


title: Tim4n_naive_b1_3

value: macrophage

tag: time (in weeks)


title: Manual2 U2OS replication timing

description: Nascent DNA

value: Early S-phase

value: Late S-phase


title: Tim4n_naive_b1_2

tag: strain


title: Genomic DNA from BLaER1 at 3h

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 3 hours

value: at 3h


title: Tim4p_ID8_4w_b4_1


title: Automated2 U2OS replication timing

description: Nascent DNA

tag: cell line


title: Automated1 U2OS replication timing

description: Nascent DNA


title: D34

hyb_protocol: Samples were hybridized onto GenomeWideSNP_6 Affymetrix Genome-Wide Human SNP 6.0 Array and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

source_name: Laterocervical lymph node

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

value: Diffuse large B cell lymphoma

value: Male

value: Frozen tissue


title: D40

source_name: Supraclavicular left lymph node

value: Diffuse large B-cell lymphoma

value: FFPE


title: Genomic DNA from BLaER1 at 12h

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 12 hours

value: at 12h

value: Female


title: D46

value: Large B-cell lymphopma with IRF4 rearrangement


title: Tim4n_ID8_8w_b6_4

value: Intra-peritoneal tumor


title: Tim4n_naive_b1_1


title: MYC2 ChIP-seq rep2

value: seedlings

value: JA 2h

value: Polyclonal anti-GFP


title: Genomic DNA from RCH-ACV at 168h

description: RCH-ACV parental cell line treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 168 hours

source_name: pre-B ALL cell line (DSMZ ACC 548)

value: at 168h

value: pre-B ALL cell line (DSMZ ACC 548)


title: D43

description: Hybridized to Affymetrix OncoScan FFPE Assay


title: MYC2 ChIP-seq rep1

value: YpET


title: Manual1 U2OS replication timing

description: Nascent DNA

value: Early S-phase

value: Late S-phase


title: Genomic DNA from BLaER1 at 72h

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 72 hours

value: at 72h

value: RCH-ACV derived cell line


title: K562 180k old cell sorting method replication timing

description: Nascent DNA


title: D38

source_name: Tonsil and submandibular lymph node


title: EH20_NKAES_5

city: Montreal

first: Panojot

last: Bifsha

state: QC

address: 3175 Chemin de la Côte Ste-Catherine

department: Pediatrics

country: Canada

institute: CHU Sainte-Justine

description: NKAES cells from resting NK cells of Donor 5

data_processing:
The sequencing files were verified using FastQC to look for any obvious bad quality libraries. The samples were then processed with TrimGalore! to remove any remaining adaptor sequences and to remove reads end with an average quality lower to Q20.
The trimmed files were then analyzed using Kallisto v0.43.0, which is using the annotated genes reported on the reference genome. The Ensembl v75 gene annotation version was used.
The differential gene expression analysis was done using the edgeR and limma R packages. A normalization using the voom function was done. The FDR correction procedure was done using the qvalue R package.
The processed data were obtained by using the tximport R package directly on the output coming from Kallisto. Those were then normalized and put to the CPM format, in order to be able to compare the samples between them.
Genome_build: hg19
Supplementary_files_format_and_content: CPMs

source_name: Peripheral blood

growth_protocol: NK resting cells were obtained from peripheral blood of adult healthy volunteers and used thereafter for total RNA purification. A subset of NK resting cells (from 4 donors) were expanded using the Amplification and Expansion System (NKAES) with irradiated K562mbIL21 feeders in RPMI1640 supplemented with 10% FCS and penicillin/streptomycin and 200 UI/mL of human recombinant IL-2.

extract_protocol:
Extraction of total RNA was done using the RNeasy mini kit (Qiagen) and manufacturer recommendations.
The quality of RNA was verified with 2100 Bioanalyzer (Agilent) prior to preparation of sequencing libraries with the TruSeq RNA Sample Prep v2 Kit from Illumina.

tag: donor

tag: developmental stage

value: Adult

tag: culture

value: K562mbIL21 expansion system (NKAES)

value: activated NK cells


title: D36

source_name: Abdominal tumor

value: High grade B-cell lymphoma, NOS

value: Male

value: FFPE


title: MISEQ_5018: Non-transgenic IgG control sample

value: Air 2h

value: Goat IgG whole molecule


title: D15

label_protocol: GenomeWideSNP_6 Affymetrix Genome-Wide Human SNP 6.0 Array

value: Large B-cell lymphopma with IRF4 rearrangement

value: Female

value: Frozen tissue


title: 180k K562 new cell sorting method replication timing

description: Nascent DNA

source_name: nascent DNA from early S-phase

tag: phase

source_name: nascent DNA from late S-phase


title: Genomic DNA from BLaER1 at 48h

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 48 hours

value: at 48h


title: Genomic DNA from BLaER1 at 24h

description: RCH-ACV transduced with inducible CEBPA treated with 27.24 ng/mL of Estradiol (100 nM), 10 ng/mL of IL3 and 10 ng/mL of M-CSF, during 24 hours

value: at 24h


title: EH16_NKAES_4

description: NKAES cells from resting NK cells of Donor 4


title: D32


title: EH10_NKAES_3

description: NKAES cells from resting NK cells of Donor 3


title: Tim4n_ID8_8w_b6_1

value: Intra-peritoneal tumor

value: macrophage


title: MV4-11 shRINF

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® HTA2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using TAC4.0 version2 software (Thermofisher).

source_name: proliferating MV4-11 shRINF

label_protocol: 400 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

growth_protocol: Human leukemic cell lines were purchased from DSMZ (MV4-11; Braunschweig, Germany) and from the American Type Culture Collection (K562; Molsheim, France). UT7 5.3 cells were kindly provided by Isabelle Dusanter-Fourt (Cochin Institute, Paris, France). K562 and MV4-11 were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 2 mM L-Glutamine, 50 U/ml penicillin G and 50 µg/ml streptomycin (Life Technologies, Saint-Aubin, France). UT7 5.3 cells were cultured in minimum essential medium (MEM) α medium containing 10% of FCS, 2 mM L-Glutamine, 50 U/ml penicillin G and 50 µg/ml streptomycin (Life Technologies, Saint-Aubin, France) and 2,5 ng/µl of GM-CSF (Myltenyi Biotech, France).

extract_protocol: Trizol extraction of total RNA coupled to RNAeasy kit (Ambion) purification was performed according to the manufacturer's instructions.

value: Hematopoietic cell line

value: shRINF


title: EH2_NKAES_1

description: NKAES cells from resting NK cells of Donor 1

value: Adult


title: D31

source_name: Cervical lymph node


title: Tim4n_ID8_8w_b6_3


title: D35


title: D30

source_name: Lymph node

value: Diffuse large B-cell lymphoma


title: EH19_NK_5

description: Resting NK cells from Donor 5

value: Resting NK cells


title: D13

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Affymetrix CytoScan HD Array arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

source_name: Supraclavicular lymph node

label_protocol: CytoScan™ Reagent Kit

value: Diffuse large B cell lymphoma


title: D27

value: Male


title: D59

description: Cytoscan HD

source_name: Kidney mass

value: High grade B-cell lymphoma, NOS


title: EH15_NK_4

description: Resting NK cells from Donor 4


title: Tim4n_ID8_6w_b5_4


title: UT7-5.3 shRINF

source_name: proliferating UT7-5.3 shRINF


title: MV4-11 shcontrol

source_name: proliferating MV4-11 shcontrol

value: shcontrol


title: Tim4n_ID8_6w_b5_2


title: Tim4n_ID8_6w_b5_3


title: K562 shRINF

source_name: proliferating K562 shRINF


title: Tim4n_ID8_6w_b5_1


title: Tim4n_ID8_4w_b4_4


title: UT7-5.3 shcontrol

source_name: proliferating UT7-5.3 shcontrol


title: Genomic DNA from BLaER1 at 0h

description: RCH-ACV transduced with inducible CEBPA without treatment

source_name: RCH-ACV derived cell line

value: at 0h

value: RCH-ACV derived cell line


title: Tim4n_ID8_8w_b6_2


title: EH9_NK_3

description: Resting NK cells from Donor 3


title: EH1_NK_1

description: Resting NK cells from Donor 1


title: D21

source_name: Tonsil

value: Large B-cell lymphopma with IRF4 rearrangement

value: FFPE


title: D23

source_name: Inguinal lymph node

value: Female


title: D62


title: D63

source_name: Laringe


title: D33

source_name: Mediastinal mass


title: D56

description: Cytoscan HD

source_name: Laterocervical lymph node

value: Frozen tissue


title: Genomic DNA from blood derived macrophages

description: Macrophages are derived from an anonymous blood donor; PBMCs were purified by Ficoll and monocytes were differentiated into Macrophages after 3 days of in vitro induction with 10 mL RPMI-1640 GlutaMAX, 10% FBS, 1X Penicillin/Streptomycin and 25 ug/mL of M-CSF

source_name: Macrophages derived from an anonymous blood donor

value: Unknown


title: D26

source_name: Spleen


title: D20

source_name: Terminal ileum


title: D25_R1

description: Cytoscan HD


title: D28

description: Affymetrix Genome-Wide Human SNP 6.0 Array

source_name: Cervical lymph node


title: D24

source_name: Lung


title: D25_R2

source_name: Abdominal mass


title: D18


title: Tim4n_ID8_4w_b4_3

value: Intra-peritoneal tumor

value: macrophage


title: K562 shcontrol

source_name: proliferating K562 shcontrol

value: Hematopoietic cell line


title: Tim4n_ID8_4w_b4_2


title: D25


title: CD64_naive_b1_4

value: peritoneal cavity

value: naive


title: D17

source_name: Liver


title: D3_R

source_name: Supraclavicular lymph node

value: Diffuse large B-cell lymphoma


title: Tim4n_ID8_4w_b4_1


title: D16


title: D1

source_name: Lymph node


title: D12


title: D8


title: D63

description: nCounter PanCancer Immune Profiling Panel

hyb_protocol: hybridization of the samples and Nanostring reporter/capture probes was performed at 65ºC for 16 hours.

scan_protocol: cartridges were scanned and counted using the Nanostring scanner at its higher resolution (555 FOVs).

data_processing: Normalitzation with nSolver Analysis Software 4.0. Standard normalization uses a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within thatsample lane.

label: Nanostring Reporter Probes

label_protocol: Samples were labeled with Nanostring Reporter Probes.

extract_protocol: Extraction of total RNA from tumor cell-rich areas using RNeasy Mini kit protocol.

value: female


title: D2

value: Male


title: D6

source_name: Axilar lymph node


title: D62

source_name: LN cervical

value: male


title: D54

source_name: right neck mass


title: D51

source_name: Tonsil


title: D49


title: CD64_naive_b1_1


title: CD64_naive_b1_2


title: D48

source_name: Right Tonsil


title: D14_R

source_name: Abdominal lymph node


title: D46


title: D5


title: D32


title: CD64_naive_b1_3


title: D23

source_name: Inguinal LN


title: CD64_ID8_8w_b6_4


title: CD64_ID8_8w_b6_3


title: CD64_ID8_8w_b6_2


title: CD64_ID8_6w_b5_4


title: CD64_ID8_8w_b6_1


title: CD64_ID8_6w_b5_3


title: D15


title: D20

source_name: terminal ileum


title: D17


title: D34

source_name: Laterocervical LN

value: Diffuse large B-cell lymhoma


title: CD64_ID8_6w_b5_1


title: CD64_ID8_6w_b5_2


title: D57

source_name: abdominal mass


title: D70

source_name: LN-axilar


title: D30

source_name: LN


title: Unind-3

city: Parkville

first: Andrew

last: Lonsdale

address: 50 Flemington Rd

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
The raw reads were quality and adapter trimmed using trimmomatic (v0.35)
The trimmed reads were mapped to the human genome (hg38) using the STAR aligner version 2.5.2a in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.5.0-p3 using GENCODE Release 20 comprehensive annotation
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file with Gene id and Gene length in the first two columns, followed by 9 columns containing counts for each sample

source_name: induced nephron progenitor

extract_protocol:
RNA were extracted using a Bioline Isolate II Mini kit
TruSeq stranded total RNA with RiboZero rRNA depletion

value: induced nephron progenitor

tag: culture media

value: HGM

tag: induced

tag: clone

value: CRL1502 clone C32


title: D29

source_name: small bowel

tag: cell type

value: FFPE


title: Unind-1


title: Ind-HGM-3

value: doxycycline


title: D26

source_name: Spleen


title: D25

source_name: cervical LN


title: Ind-HGM-2


title: E-CROPseq rep2

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: 950 Atlantic Drive

institute: Georgia Institute of Technology

data_processing:
Raw 10X genomics sequencing data was first demultiplexed of BCL files into FASTQ files by using “cellranger mkfastq”, provided by 10X cellranger software.
Reads were mapped to hg38 human reference genome with 67 additional artificial chromosomes containing gRNA sequences.
Number of UMI count of each guide RNA per cell was quantified by “cellranger count”.
Genome_build: hg38 with 67 artificial chromosomes containing gRNA sequences
Supplementary_files_format_and_content: tab-delimited text file include raw UMI counts at the gene level and 67 gRNAs for each cell

molecule: polyA RNA

source_name: HL60/S4 cell line

extract_protocol: Single-cell RNA sequencing libraries were prepared by using 10X Chromium single cell 3’ reagent kit V2 (PN-120267) and V3 chemistry (PN-1000092) with fresh cells

value: HL60/S4 cell line


title: E-CROPseq rep1


title: D18


title: CD64_ID8_4w_b4_3


title: CD64_ID8_4w_b4_2


title: CD64_ID8_4w_b4_4


title: Unind-2


title: Ind-HGM-1


title: Vector F cell line (gamma)

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Biological replicate 3, control cells

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

source_name: In vitro cultured cells

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: Mouse NCCs were growth in CDM (Fukuta et al., 2014), which contains Iscove's modified Dulbecco's medium/Ham's F-12 1∶1, 1X chemically defined lipid concentrate (GIBCO), 1X µg/ml Insulin-transferrin-selenium (Thermo Fisher Scientific), 450 µM monothioglycerol (Sigma), 5 mg/ml purified BSA (Sigma), 7 µg/ml Insulin (Thermo Fisher Scientific), and penicillin/streptomycin (Invitrogen). Culture dishes were coated with fibronectin (Corning). The medium was supplemented with EGF (R&D) and FGF2 (R&D) to modulate growth factor signals and SB431542 (SB) (Sigma) as a TGF-beta signaling pathway suppressor.

extract_protocol: DNA was extracted from cells and tumors using Dneasy Blood and Tissue Kit (QIAGEN)

value: Control cells, replicate 3

source_name: CRISPR/CAS9 engineered neural crest cells

value: WT cells transfected with gRNAs against CHD5 and ARID1A and transduced with Mycn, PCL_C


title: D13

source_name: supraclavicular LN

value: Frozen tissue


title: Vector F cell line (alpha)

description: Biological replicate 1, control cells

value: Control cells, replicate 1

value: WT cells transfected with gRNAs against CHD5 and ARID1A and transduced with Mycn, PCL_A


title: Vector F cell line (beta)

description: Biological replicate 2, control cells

value: Control cells, replicate 2

value: WT cells transfected with gRNAs against CHD5 and ARID1A and transduced with Mycn, PCL_B


title: AJJ2337

description: Biological replicate 4, tumor sample

source_name: Tumor resection

source_name: Tumor cells

value: PCL_A cells generated tumor A1


title: AJJ2347

description: Biological replicate 5, tumor sample

value: PCL_C2 cells generated tumor C2


title: CD64_ID8_4w_b4_1

value: Intra-peritoneal tumor

value: macrophage


title: Ind-NPSR-3

value: induced nephron progenitor

value: NPSR


title: AJJ2335

description: Biological replicate 3, tumor sample

value: PCL_C cells generated tumor C1


title: AJJ2329

description: Biological replicate 1, tumor sample

value: PCL_B cells generated tumor B1


title: Ind-NPSR-2

value: doxycycline

value: CRL1502 clone C32


title: Stressed_MeSCs_Replicate_1

city: Hangzhou

first: Bing

last: Zhang

state: Zhejiang

address: 600 Dunyu Road, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

data_processing:
Adaptor triming: Trim Galore! (0.4.1)
Alignment: STAR (2.5.3)
Differential Expression Analysis: DESeq2 (1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: .txt

source_name: FACS purified mouse melanocyte stem cells

extract_protocol:
RNA was isolated using RNeasy micro Kit (Qiagen), using QIAcube according to manufacturer instruction. RNA concentration and RNA integrity were determined by Bioanalyzer (Agilent, Santa Clara, CA) using the RNA 6000 Nano chip. High quality RNA samples with RNA Integrity Number ≥ 8 were used as input for RT-PCR and RNA-sequencing.
Smart-Seq V4

treatment_protocol: Injection of RTX 12 hours before harvesting

value: RTX


title: Stressed_MeSCs_Replicate_2

value: FACS purified mouse melanocyte stem cells


title: AJJ2331

description: Biological replicate 2, tumor sample

value: PCL_B cells generated tumor B2


title: Control_MeSCs_Replicate_2

value: Saline


title: Ind-NPSR-1


title: Control_MeSCs_Replicate_1


title: negative control CRAC 1

city: Edinburgh

first: Elizabeth

middle: H

last: Bayne

address: Alexander Crum Brown Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description:
cross-linked RNA
161108_K00166_0147_BHFT27BBXX_8_IL-PE-003_*_NNNGCGCAGC_L5Ac-C4

data_processing:
Processing steps were performed using the pyCRAC package version 1.2.2.7; Demultiplexing was performed using pyBarcodeFilter.py.
3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.7).
Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py.
tRNA-reads in fasta files were mapped by STAR (version 2.7.1a) and unmapped output used for further analysis steps which were done with pyCRAC version 1.4.5
Reads were mapped to the S. pombe reference genome (v2.30; source pombase) using novoalign (version 3.09.02) and feature counts were generated using pyReadCounters (version 1.4.4.) with options –blocks --mutations=delsonly
The gtf files were used to generate bedgraph files for visualisation.
Genome_build: ASM294v2.30
Supplementary_files_format_and_content: gtf and bedgraph files containing genomic positions of mapped reads after tRNA reads have been  filtered out

organism: Schizosaccharomyces pombe

source_name: negative control CRAC

growth_protocol: Cells were grown to exponential phase in PMG minus TRP medium at 32ºC

extract_protocol:
Cells (0.8-1g) were lysed in 1V (w/v) of TN150 (50 mM Tris pH 8.0, 0.1% NP-40, 150 mM NaCl, 5 mM beta-mercaptoethanol, Roche protease inhibitor cocktail) with 3V of 0.5 mm Zirkonia beads by vortexing for five minutes at full speed. Lysates were clarified by centrifugation and processed as previously described (Granneman et al PNAS 2009, doi: 10.1073/pnas.0901997106).
Libraries were constructed using the CRAC library preparation method described in Granneman et al PNAS 2009 with small modifications to the adapter sequences (see sequences below)
PCR oligonucleotides for making CRAC libraries
3' adapter:
App_PE: 5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’
5' adapters:
L5Ba: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrArGrArGrC-OH-3' (Mkt1 CRAC 1)
L5Bd: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrUrCrUrCrUrArGrCrN-OH-3' (no-tag negative control CRAC 1)
L5Aa: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrUrArArGrC-OH-3' (Mkt1 CRAC 2)
L5Ac: 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrGrCrGrCrArGrC-OH-3' (no-tag negative control CRAC 2)
P5_forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
P3_reverse: 5’-CAAGCAGAAGACGGCATACGAGAT(6nt barcode)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’

treatment_protocol: Cells were UV-irradiated in the X-Varilinker (Van Nues et al Nature Communications 2017, doi: 10.1038/s41467-017-00025-5) for 42.5 seconds in PMG minus Trp medium and harvested by filtration. Cells were snap-frozen in liquid nitrogen and stored at -80ºC.

tag: genotype

value: h+ otr1R(Sph1):ade6+ ade6-210 leu1-32 ura4D18


title: negative control CRAC 2

description:
cross-linked RNA
161108_K00166_0147_BHFT27BBXX_8_IL-PE-002_*_NNNTCTCTAGC_L5Bd-C4


title: Mkt1 CRAC 2

description:
cross-linked RNA
161108_K00166_0147_BHFT27BBXX_8_IL-PE-002_*_NNNAGAGC_L5Ba-M4

source_name: Mkt1 CRAC

value: h+ mkt1-HTP-KanR otr1R(Sph1):ade6+ ade6-210 leu1-32 ura4D18


title: Mkt1 CRAC 1

description:
cross-linked RNA
161108_K00166_0147_BHFT27BBXX_8_IL-PE-003_*_NNNTAAGC_L5Aa-M4


title: mkt1_3

description:
h+ mkt1Δ::NatR ade6-210 leu1-32 ura4-D18 otr1R(Sph1):ade6+
processed data file: WT_V_MKT1_FC.txt

data_processing:
Raw reads were filtered for quality and adapter using cutadapt (v1.8.3). Parameters were (-m 50 -q 30 -f fastq -b AGATCGGAAGAGC –B AGATCGGAAGAGC).
Trimmed reads were aligned to the S. pombe reference genome (v2.30) using STAR v2.5.
Read counts were obtained using HTSeq v.0.6.1 with mode 'union'.
Differential expression analysis was then carried out using edgeR (version 3.12.0). Genes with less than 20 reads were discarded from the analysis.
Genome_build: ASM294v2.30
Supplementary_files_format_and_content: Tab-delimited text file including log2FC values for each sample.

growth_protocol: Cells were grown in YES at 32C.

extract_protocol:
Total RNA was extracted from 1 × 10e7 cells in exponential growth phase using the Masterpure Yeast RNA Purification Kit (Epicentre) according to manufacturer's instructions.
Libraries were constructed using Illumina TruSeq stranded mRNA library preparation kit according to manufacturer’s instructions.

value: h+ mkt1<delta>::NatR ade6-210 leu1-32 ura4-D18 otr1R(Sph1):ade6+


title: GATA4-Exo,rep2

city: Nanjing

first: chunshu

last: Hao

address: No.87 Dingjiaqiao street

department: Cardiology

institute: Southeast university

hyb_protocol: Labeled miRNA was then hybridized to the array for 16 h at 48°C and 60 rpm

scan_protocol: Gene chips were then scanned by using a Hewlett Packard Gene Array Scanner G3000 7G (Affymetrix).

data_processing: Expression data were generated by using Affymetrix Expression Console software and normalized according to the RMA method. The RVM t test was applied to filter the differentially expressed genes for the control and experimental groups.

source_name: Exosome from GATA4 overespressed cardiosphere-derived cells

label_protocol: One microgram of total RNA was used as the input in the labeling reaction as recommended by the protocol of the Genisphere FlashTag Biotin RNA Labeling Kit..

extract_protocol: Total RNA was extracted from CDCs-Exo by using a Qiagen miRNeasy Mini Kit. Global expression patterns of miRNAs were then examined by using Affymetrix GeneChip miRNA 4.0 arrays.

tag: Sex

value: Male

value: myocardium

value: GATA4 overexpressed

tag: age

value: 8 weeks


title: WA09_HESC _Diff_EMIM_d4___87.2428.2.1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

description: SAMPLE 15

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R version 2.14.2

source_name: WA09_HESC _Diff_EMIM_d4

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: WA09_HESC were grown in StemPro (Invitrogen) with 12ng/mL bFGF. BEWO cells were cultured in F12 +10FBS, HTR8 in RPMI +10%FBS and JEG3 cells in DMEM +10%FBS.

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: For trophoblast differentiation, WA09_HESC cells were treated with 10ng/mL of BMP4 (R&D Systems) in minimal media composed of DMEM/F12, 2%BSA, 1% ITS, 2mM L-Glutamine, 1% non-essential aminoacids, and 0.1mM 2-mercaptoethanol for 4 days.

tag: cell/tissue type

tag: pipeline sample id


title: Stroma__Wk7.2_Tr1_P723_778.2438.1.1

description: SAMPLE 13

value: placental tissue; Stroma


title: GATA4-Exo,rep1

tag: tissue


title: GATA4-Exo,rep3


title: WA09_HESC _Diff_EMIM_d4___87.2428.1.1

description: SAMPLE 14


title: JEG3_CHORIOCA____2.2424.2.1

description: SAMPLE 12

value: Choriocarcinoma-derived cell line


title: HTR8_IMMORT_TROPH____775.2424.1.1

description: SAMPLE 9

value: Immortilised extravillous trophoblast (EVT) cells


title: HDF51_FIBRO____166.436.1.1

description: SAMPLE 8

value: Adult Dermal Fibroblast


title: HTR8_IMMORT_TROPH____775.2424.2.1

description: SAMPLE 10


title: JEG3_CHORIOCA____2.2424.1.1

description: SAMPLE 11


title: HDF51_FIBRO____166.411.1.1

description: SAMPLE 5


title: mkt1_1


title: wt_3

description: processed data file: WT_V_MKT1_FC.txt

value: h+ ade6-210 leu1-32 ura4-D18 otr1R(Sph1):ade6+


title: wt_2

description: processed data file: WT_V_MKT1_FC.txt


title: NC-Exo, rep2

source_name: Exosome from WT cardiosphere-derived cells

value: wild type


title: HDF51_FIBRO____166.411.2.1

description: SAMPLE 6


title: HDF51_FIBRO____166.411.4.1

description: SAMPLE 7


title: CTB_EGFR+ _Wk7.5_Tr1_P716_581.2431.1.1

description: SAMPLE 3

value: primary cells (first trimester CTB)


title: HT_1

description:
geneCounts_hg19_HT.txt
DESeq_hg19_HT_vs_H.csv

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the T. rubrum and hg19 genomes using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.5 (upregulation) or < -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome and hg19 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

source_name: HaCat cell line treated with terbinafine, replicate I

extract_protocol:
RNA extraction of T. rubrum and HaCat cell were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
RNA libraries were prepared for sequencing according to Illumina guidelines.

value: HaCat

tag: treatment

value: terbinafine


title: wt_1

description: processed data file: WT_V_MKT1_FC.txt

tag: strain


title: BEWO_CHORIOCA____1.2424.1.1

description: SAMPLE 1

tag: cell line

value: BeWo


title: mkt1_2


title: CTB_EGFR+ _Wk7_Tr1_P719_581.2434.1.1

description: SAMPLE 4


title: BEWO_CHORIOCA____1.2424.2.1

description: SAMPLE 2


title: COT_3

description:
geneCounts_Trub_COT.txt
geneCounts_hg19_COT.txt
DESeq_Trub_COT_vs_CO.csv
DESeq_hg19_COT_vs_CO.csv

organism:
Trichophyton rubrum
Homo sapiens

source_name: Co-culture treated with terbinafine, replicate III


title: CO_2

description:
geneCounts_Trub_CO.txt
geneCounts_hg19_CO.txt
DESeq_Trub_COT_vs_CO.csv
DESeq_hg19_COT_vs_CO.csv

source_name: Co-culture, replicate II


title: CO_1

source_name: Co-culture, replicate I


title: NC-Exo, rep3


title: H_1

description:
geneCounts_hg19_H.txt
DESeq_hg19_HT_vs_H.csv

source_name: HaCat cell line, replicate I


title: CO_3

source_name: Co-culture, replicate III


title: NC-Exo, rep1


title: COT_2

source_name: Co-culture treated with terbinafine, replicate II


title: NBN-5_03_G11

status: Public on Nov 27 2019

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

country: Germany

institute: MPI-CBG

description: counts.csv

data_processing:
FastQC was used to   examine quality of the reads after sequencing.
Alignment with GSNAP (v 2017-08-15) with parameters for sample ON15_01_G10 (all other samples accordingly): ‘gsnap.sse42 -D /projects/seq-work/user/pipeline/gmap -d GRCz10 --gunzip -A sam -t 14 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-87.ss.GRCz10.iit --read-group-id=L22281_ON15_01_G10 --read-group-name=ON15_01_G10 --read-group-library=L22281 --read-group-platform=illumina fastq/L22281_ON15_01_G10_R1.fastq.gz’
Ensembl gene annotation version 87 was used to detect exon spanning reads
featureCounts (v1.5.3) was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: "-a" "/projects/seq-work/user/pipeline/annotation/danio_rerio/GRCz10/EnsemblGene-87.GRCz10.TR.gtf" "-s" "2" "-o" "genecount/bfx811.GRCz10.e87.txt" "-Q" "1" "-T" "8" "--tmpDir" "/tmp/418815.1.ngs.q"
Genome_build: GRCz10 reference, inclusive the 92 ERCC Spike-In transcripts
Supplementary_files_format_and_content: `counts.csv` is a comma separated table and contains the raw count matrix.

organism: Danio rerio

source_name: Brain

extract_protocol:
adult zebrafish brains were collected, digested into single cells using the Papain Neural Tissue Dissociation Kit (Miltenyi) and sorted by FACS to isolate cells expressing GFP or mcherry
The Illumina Nextera DNA library preparation kit (FC-121-1031) was used to prepare libraries.

tag: sorting

value: NBN

tag: FISH id

tag: batch

tag: fraction mapped


title: NBN-5_03_B12

description: counts.csv


title: NBN-5_03_E11

description: counts.csv


title: NBN-5_03_C12

description: counts.csv


title: NBN-5_03_G12

description: counts.csv


title: NBN-5_03_A12

description: counts.csv


title: NBN-5_03_F12

description: counts.csv


title: NBN-5_03_H11

description: counts.csv


title: NBN-5_03_E12

description: counts.csv


title: NBN-5_03_F11

description: counts.csv


title: NBN-5_03_H12

description: counts.csv


title: NBN-5_03_D12

description: counts.csv


title: NBN-5_03_C11

description: counts.csv


title: NBN-5_03_G10

description: counts.csv


title: NBN-5_03_B11

description: counts.csv


title: NBN-5_03_D11

description: counts.csv


title: liver maternal high fat diet rep1

city: Beijing

first: Qian

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: maternal high fat diet

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

source_name: MeDIP DNA from maternal high fat diet

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from fat samples using Dneasy Blood & Tissue Kit.

tag: diet

value: maternal high fat diet

tag: sample type

value: MeDIP

value: liver

value: 8 week

label: Cy 3

source_name: input DNA from maternal high fat diet

value: input


title: NBN-5_03_F10

description: counts.csv


title: NBN-5_03_A11

description: counts.csv


title: liver control diet rep3

description: maternal control diet

source_name: MeDIP DNA from control diet

value: maternal control diet

source_name: input DNA from maternal control diet


title: liver control diet rep1

description: maternal control diet


title: NBN-5_03_E10

description: counts.csv


title: COT_1

first: Ana

last: Fachin

address: Av. Costabile Romano, 2201

institute: Unaerp

source_name: Co-culture treated with terbinafine, replicate I


title: NBN-5_03_H10

description: counts.csv


title: NBN-5_03_F09

description: counts.csv


title: RG-5_03_D09

description: counts.csv

value: RG


title: liver control diet rep2

description: maternal control diet


title: RG-5_03_C09

description: counts.csv


title: liver maternal high fat diet rep3

description: maternal high fat diet


title: NBN-5_03_A10

description: counts.csv


title: RG-5_03_A09

description: counts.csv


title: NBN-5_03_H09

description: counts.csv


title: RG-5_03_B09

description: counts.csv


title: RG-5_03_H08

description: counts.csv


title: RG-5_03_A08

description: counts.csv


title: RG-5_03_F08

description: counts.csv


title: RG-5_03_B08

description: counts.csv


title: NBN-5_03_B10

description: counts.csv


title: NBN-5_03_G09

description: counts.csv


title: RG-5_03_E08

description: counts.csv


title: RG-5_03_E09

description: counts.csv


title: RG-5_03_G08

description: counts.csv


title: NBN-5_03_D10

description: counts.csv


title: RG-5_03_D08

description: counts.csv


title: RG-5_03_H07

description: counts.csv


title: RG-5_03_F07

description: counts.csv


title: RG-5_03_A07

description: counts.csv


title: RG-5_03_C08

description: counts.csv


title: RG-5_03_G07

description: counts.csv


title: NBN-5_03_C10

description: counts.csv


title: RG-5_03_H06

description: counts.csv


title: RG-5_03_F06

description: counts.csv


title: RG-5_03_G06

description: counts.csv


title: RG-5_03_E07

description: counts.csv


title: RG-5_03_D07

description: counts.csv


title: RG-5_03_C06

description: counts.csv


title: RG-5_03_D06

description: counts.csv


title: RG-5_03_B06

description: counts.csv


title: RG-5_03_B07

description: counts.csv


title: RG-5_03_C07

description: counts.csv


title: RG-5_03_E06

description: counts.csv


title: NBN-4_03_A05

description: counts.csv


title: NBN-4_03_B04

description: counts.csv


title: NBN-4_03_E05

description: counts.csv


title: NBN-4_03_D05

description: counts.csv


title: NBN-4_03_B05

description: counts.csv


title: NBN-4_03_F05

description: counts.csv


title: NBN-4_03_G03

description: counts.csv


title: NBN-4_03_C05

description: counts.csv


title: NBN-4_03_H04

description: counts.csv


title: NBN-4_03_C04

description: counts.csv


title: NBN-4_03_H03

description: counts.csv


title: NBN-4_03_A04

description: counts.csv


title: NBN-4_03_F04

description: counts.csv


title: NBN-4_03_E04

description: counts.csv


title: NBN-4_03_G04

description: counts.csv


title: NBN-4_03_F03

description: counts.csv


title: NBN-4_03_D04

description: counts.csv


title: NBN-4_03_E03

description: counts.csv


title: NBN-4_03_C03

description: counts.csv


title: NBN-4_03_B03

description: counts.csv


title: RG-4_03_B02

description: counts.csv


title: NBN-4_03_A03

description: counts.csv


title: NBN-4_03_D02

description: counts.csv


title: RG-4_03_A02

description: counts.csv


title: NBN-4_03_E02

description: counts.csv


title: NBN-4_03_C02

description: counts.csv


title: NBN-4_03_G02

description: counts.csv


title: NBN-4_03_D03

description: counts.csv


title: NBN-4_03_F02

description: counts.csv


title: RG-4_03_G01

description: counts.csv


title: RG-4_03_H01

description: counts.csv


title: RG-4_03_E01

description: counts.csv


title: RG-4_03_F01

description: counts.csv


title: RG-4_03_B01

description: counts.csv


title: liver maternal high fat diet rep2

description: maternal high fat diet


title: RG-4_03_C01

description: counts.csv


title: RG-4_03_A01

description: counts.csv


title: RG-4_02_D12

description: counts.csv


title: RG-4_02_G11

description: counts.csv


title: RG-4_02_B12

description: counts.csv


title: RG-4_02_C12

description: counts.csv


title: RG-4_03_D01

description: counts.csv


title: RG-4_02_A12

description: counts.csv


title: NBN-4_03_H02

description: counts.csv


title: RG-4_02_G12

description: counts.csv


title: RG-4_02_C11

description: counts.csv


title: RG-4_02_H12

description: counts.csv


title: RG-4_02_F11

description: counts.csv


title: NBN-3_02_D10

description: counts.csv


title: RG-4_02_D11

description: counts.csv


title: RG-4_02_E11

description: counts.csv


title: RG-4_02_E12

description: counts.csv


title: NBN-3_02_F10

description: counts.csv


title: NBN-3_02_C10

description: counts.csv


title: RG-4_02_H11

description: counts.csv


title: RG-4_02_A11

description: counts.csv


title: RG-4_02_B11

description: counts.csv


title: RG-4_02_G10

description: counts.csv


title: NBN-3_02_E10

description: counts.csv


title: NBN-3_02_F09

description: counts.csv


title: NBN-3_02_H09

description: counts.csv


title: NBN-3_02_E09

description: counts.csv


title: NBN-3_02_A10

description: counts.csv


title: NBN-3_02_B10

description: counts.csv


title: RG-4_02_F12

description: counts.csv


title: NBN-3_02_D09

description: counts.csv


title: NBN-3_02_C09

description: counts.csv


title: NBN-3_02_H08

description: counts.csv


title: NBN-3_02_B09

description: counts.csv


title: NBN-3_02_H07

description: counts.csv


title: NBN-3_02_C08

description: counts.csv


title: NBN-3_02_B08

description: counts.csv


title: NBN-3_02_D08

description: counts.csv


title: RG-3_02_F06

description: counts.csv


title: NBN-3_02_E07

description: counts.csv


title: NBN-3_02_F08

description: counts.csv


title: RG-3_02_B07

description: counts.csv


title: NBN-3_02_A08

description: counts.csv


title: RG-4_02_H10

description: counts.csv


title: NBN-3_02_C07

description: counts.csv


title: NBN-3_02_G09

description: counts.csv


title: NBN-3_02_G08

description: counts.csv


title: NBN-3_02_D07

description: counts.csv


title: RG-3_02_E06

description: counts.csv


title: NBN-3_02_E08

description: counts.csv


title: NBN-3_02_F07

description: counts.csv


title: RG-3_02_D06

description: counts.csv


title: NBN-3_02_G07

description: counts.csv


title: NBN-3_02_A09

description: counts.csv


title: RG-3_02_C06

description: counts.csv


title: RG-3_02_G06

description: counts.csv


title: RG-3_02_B05

description: counts.csv


title: RG-3_02_B06

description: counts.csv


title: RG-3_02_A06

description: counts.csv


title: RG-3_02_C05

description: counts.csv


title: RG-3_02_H05

description: counts.csv


title: RG-3_02_E04

description: counts.csv


title: RG-3_02_E05

description: counts.csv


title: RG-3_02_G04

description: counts.csv


title: RG-3_02_F04

description: counts.csv


title: RG-3_02_F05

description: counts.csv


title: RG-3_02_H03

description: counts.csv


title: RG-3_02_G03

description: counts.csv


title: RG-3_02_D05

description: counts.csv


title: RG-3_02_B04

description: counts.csv


title: RG-3_02_A07

description: counts.csv


title: NBN-2_02_B03

description: counts.csv


title: RG-3_02_C04

description: counts.csv


title: RG-3_02_H06

description: counts.csv


title: NBN-2_02_H02

description: counts.csv


title: RG-3_02_A04

description: counts.csv


title: NBN-2_02_G02

description: counts.csv


title: NBN-2_02_H01

description: counts.csv


title: NBN-2_02_C02

description: counts.csv


title: RG-3_02_H04

description: counts.csv


title: NBN-2_02_E02

description: counts.csv


title: NBN-2_02_C03

description: counts.csv


title: RG-3_02_A05

description: counts.csv


title: NBN-2_02_A03

description: counts.csv


title: NBN-2_02_F02

description: counts.csv


title: NBN-2_02_B02

description: counts.csv


title: RG-3_02_G05

description: counts.csv


title: NBN-2_02_E01

description: counts.csv


title: NBN-2_02_A02

description: counts.csv


title: NBN-2_01_G12

description: counts.csv


title: NBN-2_02_G01

description: counts.csv


title: NBN-2_02_F01

description: counts.csv


title: NBN-2_01_H12

description: counts.csv


title: NBN-2_01_E12

description: counts.csv


title: NBN-2_02_A01

description: counts.csv


title: NBN-2_02_B01

description: counts.csv


title: NBN-2_01_F12

description: counts.csv


title: NBN-2_02_C01

description: counts.csv


title: NBN-2_01_C12

description: counts.csv


title: NBN-2_01_D12

description: counts.csv


title: RG-2_01_F11

description: counts.csv


title: RG-2_01_G11

description: counts.csv


title: RG-2_01_E11

description: counts.csv


title: RG-2_01_D11

description: counts.csv


title: NBN-2_02_D02

description: counts.csv


title: NBN-2_01_B12

description: counts.csv


title: RG-2_01_C11

description: counts.csv


title: RG-2_01_B11

description: counts.csv


title: RG-2_01_E10

description: counts.csv


title: NBN-2_02_D01

description: counts.csv


title: RG-2_01_H10

description: counts.csv


title: RG-2_01_A11

description: counts.csv


title: RG-2_01_G10

description: counts.csv


title: RG-2_01_A10

description: counts.csv


title: RG-2_01_G09

description: counts.csv


title: RG-2_01_B10

description: counts.csv


title: RG-2_01_D10

description: counts.csv


title: RG-2_01_C10

description: counts.csv


title: RG-2_01_H09

description: counts.csv


title: NBN-2_01_A12

description: counts.csv


title: NBN-2_01_H11

description: counts.csv


title: RG-2_01_B09

description: counts.csv


title: RG-2_01_E09

description: counts.csv


title: RG-2_01_F09

description: counts.csv


title: RG-2_01_D09

description: counts.csv


title: RG-2_01_H08

description: counts.csv


title: RG-2_01_G08

description: counts.csv


title: RG-2_01_C09

description: counts.csv


title: RG-2_01_A09

description: counts.csv


title: RG-2_01_F10

description: counts.csv


title: RG-3_02_D04

description: counts.csv


title: RG-2_01_E08

description: counts.csv


title: NBN-1_01_F07

description: counts.csv


title: RG-2_01_D08

description: counts.csv


title: NBN-1_01_H07

description: counts.csv


title: NBN-1_01_G07

description: counts.csv


title: NBN-1_01_G04

description: counts.csv


title: NBN-1_01_D06

description: counts.csv


title: NBN-1_01_C06

description: counts.csv


title: NBN-1_01_B06

description: counts.csv


title: NBN-1_01_C07

description: counts.csv


title: NBN-1_01_H04

description: counts.csv


title: NBN-1_01_E06

description: counts.csv


title: NBN-1_01_H06

description: counts.csv


title: NBN-1_01_G06

description: counts.csv


title: NBN-1_01_A07

description: counts.csv


title: NBN-1_01_A05

description: counts.csv


title: NBN-1_01_E07

description: counts.csv


title: NBN-1_01_A06

description: counts.csv


title: NBN-1_01_D07

description: counts.csv


title: RG-1_01_D04

description: counts.csv


title: NBN-1_01_E04

description: counts.csv


title: RG-1_01_C04

description: counts.csv


title: NBN-1_01_F04

description: counts.csv


title: RG-2_01_F08

description: counts.csv


title: NBN-1_01_B05

description: counts.csv


title: RG-1_01_B04

description: counts.csv


title: NBN-1_01_D05

description: counts.csv


title: NBN-1_01_F05

description: counts.csv


title: RG-1_01_G03

description: counts.csv


title: RG-1_01_H03

description: counts.csv


title: NBN-1_01_C05

description: counts.csv


title: NBN-1_01_H05

description: counts.csv


title: RG-1_01_F03

description: counts.csv


title: RG-1_01_D03

description: counts.csv


title: RG-1_01_E03

description: counts.csv


title: RG-1_01_A03

description: counts.csv


title: RG-1_01_B03

description: counts.csv


title: NBN-1_01_F06

description: counts.csv


title: NBN-1_01_G05

description: counts.csv


title: RG-1_01_A04

description: counts.csv


title: RG-1_01_C03

description: counts.csv


title: RG-1_01_H02

description: counts.csv


title: RG-1_01_B01

description: counts.csv


title: RG-1_01_E01

description: counts.csv


title: RG-1_01_C02

description: counts.csv


title: RG-1_01_A02

description: counts.csv


title: RG-1_01_G01

description: counts.csv


title: RG-1_01_D01

description: counts.csv


title: RG-1_01_H01

description: counts.csv


title: RG-1_01_D02

description: counts.csv


title: NBN-1_01_E05

description: counts.csv


title: RG-1_01_F01

description: counts.csv


title: RG-1_01_E02

description: counts.csv


title: RG-1_01_B02

description: counts.csv


title: ON30_01_F12

description: counts.csv

value: MN


title: RG-1_01_A01

description: counts.csv


title: RG31_01_H12

description: counts.csv


title: RG-1_01_G02

description: counts.csv


title: ON29_01_E12

description: counts.csv


title: ON28_01_D12

description: counts.csv


title: ON27_01_C12

description: counts.csv


title: RG-1_01_F02

description: counts.csv


title: ON26_01_B12

description: counts.csv


title: ON25_01_A12

description: counts.csv


title: ON20_01_D11

description: counts.csv


title: NBN-1_01_B07

description: counts.csv


title: ON18_01_B11

description: counts.csv


title: ON23_01_G11

description: counts.csv


title: ON22_01_F11

description: counts.csv


title: ON11_01_C10

description: counts.csv


title: ON16_01_H10

description: counts.csv


title: ON19_01_C11

description: counts.csv


title: ON15_01_G10

description: counts.csv


title: RG-1_01_C01

description: counts.csv


title: ON14_01_F10

description: counts.csv


title: ON10_01_B10

description: counts.csv


title: ON13_01_E10

description: counts.csv


title: ON12_01_D10

description: counts.csv


title: ON05_01_E09

description: counts.csv


title: ON04_01_D09

description: counts.csv


title: ON01_01_A09

description: counts.csv


title: ON09_01_A10

description: counts.csv


title: ON08_01_H09

description: counts.csv


title: ON24_01_H11

description: counts.csv


title: ON03_01_C09

description: counts.csv


title: ON02_01_B09

description: counts.csv


title: NBN29_01_F08

description: counts.csv


title: NBN30_01_G08

description: counts.csv


title: NBN27_01_D08

description: counts.csv


title: NBN28_01_E08

description: counts.csv


title: NBN23_01_H07

description: counts.csv


title: NBN22_01_G07

description: counts.csv


title: ON17_01_A11

description: counts.csv


title: NBN21_01_F07

description: counts.csv


title: NBN26_01_C08

description: counts.csv


title: ON21_01_E11

description: counts.csv


title: NBN18_01_B07

description: counts.csv


title: ON07_01_G09

description: counts.csv


title: ON06_01_F09

description: counts.csv


title: NBN25_01_B08

description: counts.csv


title: NBN10_01_A06

description: counts.csv


title: NBN16_01_H06

description: counts.csv


title: NBN17_01_A07

description: counts.csv


title: NBN14_01_F06

description: counts.csv


title: NBN20_01_D07

description: counts.csv


title: NBN02_01_H04

description: counts.csv


title: NBN11_01_B06

description: counts.csv


title: NBN15_01_G06

description: counts.csv


title: NBN12_01_C06

description: counts.csv


title: NBN01_01_G04

description: counts.csv


title: NBN13_01_D06

description: counts.csv


title: RG28_01_D04

description: counts.csv


title: RG27_01_C04

description: counts.csv


title: RG26_01_B04

description: counts.csv


title: NBN07_01_F05

description: counts.csv


title: NBN09_01_H05

description: counts.csv


title: RG25_01_A04

description: counts.csv


title: NBN04_01_B05

description: counts.csv


title: NBN08_01_G05

description: counts.csv


title: NBN03_01_A05

description: counts.csv


title: RG22_01_F03

description: counts.csv


title: NBN19_01_C07

description: counts.csv


title: RG24_01_H03

description: counts.csv


title: RG23_01_G03

description: counts.csv


title: RG20_01_D03

description: counts.csv


title: RG21_01_E03

description: counts.csv


title: RG19_01_C03

description: counts.csv


title: RG17_01_A03

description: counts.csv


title: RG18_01_B03

description: counts.csv


title: RG30_01_F04

description: counts.csv


title: NBN05_01_C05

description: counts.csv


title: RG16_01_H02

description: counts.csv


title: RG4_01_D01

description: counts.csv


title: RG15_01_G02

description: counts.csv


title: NBN06_01_D05

description: counts.csv


title: NBN24_01_A08

description: counts.csv


title: RG7_01_G01

description: counts.csv


title: RG3_01_C01

description: counts.csv


title: RG9_01_A02

description: counts.csv


title: RG2_01_B01

description: counts.csv


title: RG10_01_B02

description: counts.csv


title: RG6_01_F01

description: counts.csv


title: RG12_01_D02

description: counts.csv


title: RG5_01_E01

description: counts.csv


title: RG8_01_H01

description: counts.csv


title: RG1_01_A01

description: counts.csv


title: RG11_01_C02

description: counts.csv


title: RG13_01_E02

description: counts.csv


title: RGC061616p9_H9_S285

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution.  Single cell suspensions were incubated with 0.5ul of anti-CD90 (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl.  Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high Cd90 and GFP co-expression.  Singe cells were sorted into 2ul lysis buffer per well in multiple 96 well plates, spun down for 1min and immediated placed on dry ice, then stored at -80oC until subsequent processing for Smartseq2
We generated single cell RNA-Seq libraries using a modified Smart-seq2 method [Picelli et al., 2013, Ding et al., 2019] with the following minor change. We added 3 µl instead of 4 µl of master mix containing only 1.7 µl instead of 2.7 µl of 1 M Trehalose (Sigma-Aldrich) directly to the 2 µl cell lysate without a SPRI bead cleanup step.
Smart-seq2 per Picelli et al., 2013 with minor modifications (see above)

treatment_protocol: W3-GFP mice mice were used.  Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

tag: mouse line

value: postnatal day 15

value: retinas


title: RGC061616p9_H12_S288


title: RGC061616p9_H7_S283


title: RG14_01_F02

description: counts.csv


title: RGC061616p9_G11_S275


title: RGC061616p9_G8_S272


title: RGC061616p9_G3_S267


title: RGC061616p9_H2_S278


title: RGC061616p9_G4_S268


title: RGC061616p9_F8_S260


title: RGC061616p9_F7_S259


title: RGC061616p9_G6_S270


title: RGC061616p9_G9_S273


title: RGC061616p9_G5_S269


title: RGC061616p9_G1_S265


title: RGC061616p9_F6_S258


title: RGC061616p9_E9_S249


title: RGC061616p9_E7_S247


title: RG29_01_E04

description: counts.csv


title: RGC061616p9_F3_S255


title: RGC061616p9_G2_S266


title: RGC061616p9_E6_S246


title: RGC061616p9_F9_S261


title: RGC061616p9_E4_S244


title: RGC061616p9_H3_S279


title: RGC061616p9_E3_S243


title: RGC061616p9_F1_S253


title: RGC061616p9_F4_S256


title: RGC061616p9_F11_S263


title: RGC061616p9_F12_S264


title: RGC061616p9_E1_S241


title: RGC061616p9_E2_S242


title: RGC061616p9_D6_S234


title: RGC061616p9_E11_S251


title: RGC061616p9_D8_S236


title: RGC061616p9_D7_S235


title: RGC061616p9_D5_S233


title: RGC061616p9_D4_S232


title: RGC061616p9_D12_S240


title: RGC061616p9_C6_S222


title: RGC061616p9_D10_S238


title: RGC061616p9_C3_S219


title: RGC061616p9_C12_S228


title: RGC061616p9_D3_S231


title: RGC061616p9_E8_S248


title: RGC061616p9_D2_S230


title: RGC061616p9_B8_S212


title: RGC061616p9_C10_S226


title: RGC061616p9_B5_S209


title: RGC061616p9_B4_S208


title: RGC061616p9_C7_S223


title: RGC061616p9_B6_S210


title: RGC061616p9_B2_S206


title: RGC061616p9_B7_S211


title: RGC061616p9_B12_S216


title: RGC061616p9_B11_S215


title: RGC061616p9_A8_S200


title: RGC061616p9_A9_S201


title: RGC061616p9_A5_S197


title: RGC061616p9_A4_S196


title: RGC061616p9_A7_S199


title: RGC061616p9_A2_S194


title: RGC061616p9_A12_S204


title: RGC061616p9_A3_S195


title: RGC061616p9_B10_S214


title: RGC061616p7_H5_S377


title: RGC061616p9_A10_S202


title: RGC061616p9_A1_S193


title: RGC061616p9_B3_S207


title: RGC061616p7_H11_S383


title: RGC061616p7_H10_S382


title: RGC061616p7_H1_S373


title: RGC061616p7_H12_S384


title: RGC061616p7_H2_S374


title: RGC061616p7_G6_S366


title: RGC061616p7_G5_S365


title: RGC061616p7_G3_S363


title: RGC061616p7_G7_S367


title: RGC061616p7_G9_S369


title: RGC061616p7_G11_S371


title: RGC061616p7_G8_S368


title: RGC061616p7_G1_S361


title: RGC061616p7_G2_S362


title: RGC061616p7_F3_S351


title: RGC061616p7_F4_S352


title: RGC061616p7_F2_S350


title: RGC061616p7_G10_S370


title: RGC061616p7_H3_S375


title: RGC061616p7_F11_S359


title: RGC061616p7_E7_S343


title: RGC061616p7_E8_S344


title: RGC061616p7_E5_S341


title: RGC061616p7_F5_S353


title: RGC061616p7_E6_S342


title: RGC061616p7_H7_S379


title: RGC061616p7_E4_S340


title: RGC061616p7_D8_S332


title: RGC061616p7_D9_S333


title: RGC061616p7_D6_S330


title: RGC061616p7_D4_S328


title: RGC061616p7_E2_S338


title: RGC061616p7_E3_S339


title: RGC061616p7_C9_S321


title: RGC061616p7_E1_S337


title: RGC061616p7_C7_S319


title: RGC061616p7_D5_S329


title: RGC061616p7_C6_S318


title: RGC061616p7_C5_S317


title: RGC061616p7_F6_S354


title: RGC061616p7_C1_S313


title: RGC061616p7_C11_S323


title: RGC061616p7_C12_S324


title: RGC061616p7_B4_S304


title: RGC061616p7_B6_S306


title: RGC061616p7_B9_S309


title: RGC061616p7_B12_S312


title: RGC061616p7_B11_S311


title: RGC061616p7_A8_S296


title: RGC061616p7_B10_S310


title: RGC061616p7_D1_S325


title: RGC061616p7_C8_S320


title: RGC061616p7_A6_S294


title: RGC061616p7_A5_S293


title: RGC061616p7_A4_S292


title: RGC061616p7_A2_S290


title: RGC061616p5_G9_S273


title: RGC061616p7_A11_S299


title: RGC061616p5_F9_S261


title: RGC061616p7_C2_S314


title: RGC061616p7_A1_S289


title: RGC061616p7_A10_S298


title: RGC061616p5_E10_S250


title: RGC061616p5_D8_S236


title: RGC061616p5_E6_S246


title: RGC061616p5_F4_S256


title: RGC061616p7_B3_S303


title: RGC061616p5_D3_S231


title: RGC061616p7_A9_S297


title: RGC061616p5_D1_S229


title: RGC061616p5_C5_S221


title: RGC061616p5_C4_S220


title: RGC061616p5_C8_S224


title: RGC061616p5_F11_S263


title: RGC061616p5_B7_S211


title: RGC061616p5_C2_S218


title: RGC061616p5_C3_S219


title: RGC061616p5_B3_S207


title: RGC061616p5_E7_S247


title: RGC061616p5_B4_S208


title: RGC061616p5_B6_S210


title: RGC061616p7_A3_S291


title: RGC061616p5_B2_S206


title: RGC061616p5_B1_S205


title: RGC061616p5_A1_S193


title: RGC061616p5_A4_S196


title: RGC061616p4_H5_S185


title: RGC061616p5_A12_S204


title: RGC061616p4_H8_S188


title: RGC061616p5_A2_S194


title: RGC061616p4_G7_S175


title: RGC061616p4_G3_S171


title: RGC061616p4_G4_S172


title: RGC061616p5_D10_S238


title: RGC061616p4_G2_S170


title: RGC061616p4_F7_S163


title: RGC061616p4_G1_S169


title: RGC061616p4_F4_S160


title: RGC061616p4_F3_S159


title: RGC061616p4_F12_S168


title: RGC061616p4_F2_S158


title: RGC061616p4_E6_S150


title: RGC061616p5_B11_S215


title: RGC061616p5_A6_S198


title: RGC061616p4_D12_S144


title: RGC061616p4_C2_S122


title: RGC061616p4_B11_S119


title: RGC061616p4_B1_S109


title: RGC061616p4_D2_S134


title: RGC061616p3_H3_S87


title: RGC061616p3_G6_S78


title: RGC061616p3_H7_S91


title: RGC061616p3_G1_S73


title: RGC061616p3_F6_S66


title: RGC061616p3_F12_S72


title: RGC061616p3_G5_S77


title: RGC061616p3_G2_S74


title: RGC061616p4_A7_S103


title: RGC061616p3_F5_S65


title: RGC061616p4_B8_S116


title: RGC061616p3_F2_S62


title: RGC061616p3_F4_S64


title: RGC061616p3_E2_S50


title: RGC061616p3_E5_S53


title: RGC061616p4_D6_S138


title: RGC061616p3_E12_S60


title: RGC061616p3_E11_S59


title: RGC061616p4_E11_S155


title: RGC061616p3_C8_S32


title: RGC061616p3_B8_S20


title: RGC061616p3_B3_S15


title: RGC061616p3_C1_S25


title: RGC061616p3_D1_S37


title: RGC061616p3_C2_S26


title: RGC061616p3_B12_S24


title: RGC061616p3_B11_S23


title: RGC061616p3_A12_S12


title: RGC061616p3_C7_S31


title: RGC061616p2_H8_S188


title: RGC061616p3_A2_S2


title: RGC061616p3_A3_S3


title: RGC061616p3_E1_S49


title: RGC061616p2_H6_S186


title: RGC061616p2_H5_S185


title: RGC061616p2_H3_S183


title: RGC061616p2_H7_S187


title: RGC061616p2_H9_S189


title: RGC061616p2_H2_S182


title: RGC061616p2_G8_S176


title: RGC061616p2_H11_S191


title: RGC061616p2_H1_S181


title: RGC061616p2_G1_S169


title: RGC061616p2_G11_S179


title: RGC061616p2_G5_S173


title: RGC061616p3_D9_S45


title: RGC061616p2_G9_S177


title: RGC061616p2_G10_S178


title: RGC061616p2_F9_S165


title: RGC061616p2_F8_S164


title: RGC061616p2_F5_S161


title: RGC061616p2_F4_S160


title: RGC061616p2_F2_S158


title: RGC061616p2_F3_S159


title: RGC061616p2_F1_S157


title: RGC061616p2_E8_S152


title: RGC061616p2_F12_S168


title: RGC061616p2_E6_S150


title: RGC061616p2_F10_S166


title: RGC061616p2_E5_S149


title: RGC061616p2_E4_S148


title: RGC061616p2_E2_S146


title: RGC061616p2_E12_S156


title: RGC061616p2_E11_S155


title: RGC061616p2_D7_S139


title: RGC061616p2_D9_S141


title: RGC061616p2_E3_S147


title: RGC061616p2_D4_S136


title: RGC061616p2_C8_S128


title: RGC061616p2_C7_S127


title: RGC061616p2_D1_S133


title: RGC061616p2_C6_S126


title: RGC061616p2_C9_S129


title: RGC061616p2_D12_S144


title: RGC061616p2_D10_S142


title: RGC061616p2_C1_S121


title: RGC061616p2_C2_S122


title: RGC061616p2_C5_S125


title: RGC061616p2_E9_S153


title: RGC061616p2_C12_S132


title: RGC061616p2_C11_S131


title: RGC061616p2_B8_S116


title: RGC061616p2_B5_S113


title: RGC061616p2_D8_S140


title: RGC061616p2_B6_S114


title: RGC061616p2_D2_S134


title: RGC061616p2_B1_S109


title: RGC061616p2_B10_S118


title: RGC061616p2_B2_S110


title: RGC061616p2_B3_S111


title: RGC061616p2_A8_S104


title: RGC061616p2_A7_S103


title: RGC061616p2_A6_S102


title: RGC061616p2_B7_S115


title: RGC061616p2_A10_S106


title: RGC061616p2_A4_S100


title: RGC061616p2_C3_S123


title: RGC061616p1_H5_S89


title: RGC061616p2_A11_S107


title: RGC061616p2_A1_S97


title: RGC061616p1_H4_S88


title: RGC061616p1_H2_S86


title: RGC061616p1_H12_S96


title: RGC061616p1_H1_S85


title: RGC061616p2_B11_S119


title: RGC061616p2_B4_S112


title: RGC061616p1_H11_S95


title: RGC061616p1_H10_S94


title: RGC061616p1_G9_S81


title: RGC061616p1_G8_S80


title: RGC061616p1_G5_S77


title: RGC061616p1_G7_S79


title: RGC061616p2_A9_S105


title: RGC061616p1_H3_S87


title: RGC061616p1_G2_S74


title: RGC061616p1_G3_S75


title: RGC061616p1_F8_S68


title: RGC061616p2_A12_S108


title: RGC061616p1_F9_S69


title: RGC061616p2_A2_S98


title: RGC061616p1_G11_S83


title: RGC061616p1_H8_S92


title: RGC061616p1_F7_S67


title: RGC061616p1_F2_S62


title: RGC061616p1_E7_S55


title: RGC061616p1_F10_S70


title: RGC061616p1_E4_S52


title: RGC061616p1_F12_S72


title: RGC061616p1_F5_S65


title: RGC061616p1_E8_S56


title: RGC061616p1_E2_S50


title: RGC061616p1_E3_S51


title: RGC061616p1_D3_S39


title: RGC061616p1_D5_S41


title: RGC061616p1_D7_S43


title: RGC061616p1_D9_S45


title: RGC061616p1_G4_S76


title: RGC061616p1_D8_S44


title: RGC061616p1_D10_S46


title: RGC061616p1_D2_S38


title: RGC061616p1_D1_S37


title: RGC061616p1_C7_S31


title: RGC061616p1_C12_S36


title: RGC061616p1_C10_S34


title: RGC061616p1_B2_S14


title: RGC061616p1_B8_S20


title: RGC061616p10_H9_S381


title: RGC061616p1_B1_S13


title: RGC061616p10_H7_S379


title: RGC061616p1_E1_S49


title: RGC061616p10_H8_S380


title: RGC061616p10_H6_S378


title: RGC061616p1_E11_S59


title: RGC061616p1_C9_S33


title: RGC061616p10_H5_S377


title: RGC061616p10_H4_S376


title: RGC061616p10_H2_S374


title: RGC061616p10_G8_S368


title: RGC061616p10_G7_S367


title: RGC061616p10_G5_S365


title: RGC061616p10_H10_S382


title: RGC061616p10_H1_S373


title: RGC061616p10_G2_S362


title: RGC061616p10_F4_S352


title: RGC061616p10_G3_S363


title: RGC061616p10_G10_S370


title: RGC061616p10_G11_S371


title: RGC061616p10_F3_S351


title: RGC061616p10_F1_S349


title: RGC061616p10_E9_S345


title: RGC061616p10_F12_S360


title: RGC061616p10_F10_S358


title: RGC061616p10_E8_S344


title: RGC061616p10_E6_S342


title: RGC061616p10_E2_S338


title: RGC061616p10_E10_S346


title: RGC061616p10_D7_S331


title: RGC061616p10_E11_S347


title: RGC061616p10_D9_S333


title: RGC061616p10_E3_S339


title: RGC061616p10_E7_S343


title: RGC061616p10_D8_S332


title: RGC061616p10_D5_S329


title: RGC061616p10_D11_S335


title: RGC061616p10_D10_S334


title: RGC061616p10_D6_S330


title: RGC061616p10_G1_S361


title: RGC061616p10_C7_S319


title: RGC061616p10_D4_S328


title: RGC061616p10_C9_S321


title: RGC061616p10_C6_S318


title: RGC061616p10_C5_S317


title: RGC061616p10_C2_S314


title: RGC061616p10_C1_S313


title: RGC061616p10_C12_S324


title: RGC061616p10_C3_S315


title: RGC061616p10_C11_S323


title: RGC061616p10_C10_S322


title: RGC061616p10_C4_S316


title: RGC061616p10_B9_S309


title: RGC061616p10_B2_S302


title: RGC061616p10_B1_S301


title: RGC061616p10_B8_S308


title: RGC061616p10_B12_S312


title: RGC061616p10_B11_S311


title: RGC061616p10_B10_S310


title: RGC061616p10_A8_S296


title: RGC061616p10_A7_S295


title: RGC061616p10_A6_S294


title: RGC061616p10_A2_S290


title: RGC061616p10_A4_S292


title: RGC061616p10_A10_S298


title: RGC061616p10_A1_S289


title: RGC061616p10_A3_S291


title: RGC061616p10_A12_S300


title: ChIP-seq-PolII-late-g1-rep1

city: Philadelphia

first: Gerd

middle: A

last: Blobel

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

institute: University of Pennsylvania	Children's Hospital of Philadelphia

data_processing:
Sequencing reads were mapped to the reference mouse genome mm9 using bowtie (0.12.7, "-m 2 --tryhard"). Reads were filtered to remove non-uniquely mapped reads and PCR duplicates using SAMtools (v1.7, "samtools rmdup -s") and converted to bed format using BEDtools (v2.27.1, "bedtools bamtobed"). Peaks were identified using the MACS2 (v2.1.0, "macs2 callpeak") with punctate calling for both CTCF and Rad21 (p-values 1e-8 and 1e-4 respectively), using each IP's cell cycle stage matched input as the control.
Genome_build: mm9

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
For each IP, 7-10million crosslinked cells were re-suspended in 1ml Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) containing fresh protease inhibitors (Sigma P8340) and 1mM phenylmethylsulfonyl fluoride (PMSF) for 20min on ice. Nuclei was pelleted at 4℃ and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS) containing fresh protease inhibitors and PMSF and incubated for 20min on ice. Samples were added with 0.6ml IP Dilution Buffer (20mM Tris pH 8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing fresh protease inhibitor and PMSF and then subject to sonication for 45min (Epishear, Active Motif, 100% amplitude, 30s ON and 30s OFF, ~45min). After sonication, samples were spun at 21130g at 4℃ for 10min to pellet cell debris. Supernatant was transferred to a new tube and supplemented with 3.4ml IP Dilution Buffer containing fresh protease inhibitor, PMSF, protein A/G agarose beads (prepared by mixing protein A (Thermo Fisher Scientific 15918014) and protein G (Thermo Fisher Scientific 15920010) agarose beads at 1:1 ratio) and 50mg isotope matched IgG. Chromatin preclear was carried out for over 2h at 4℃. 200ml (4%) of precleared chromatin was taken out from subsequent IP steps and set as input. Pre-cleared chromatin was then added to protein A/C beads bound with antibodies and incubated overnight with rotation at 4℃. After IP, beads were washed once with IP Wash Buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with PE Buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing and pelleting steps were performed on ice or at 4℃. Beads were then moved to room temperature and eluted twice with 100ml freshly prepared Elution Buffer (100mM NaHCO3, 1%SDS) to reach a final concentration of 200ml. Eluted samples were supplemented with 12ml 5M NaCl, 2ml DNase-free RNaseA (10mg/ml, 10109169001 BMB) and incubated at 65℃ for overnight. Samples were then added with 3ml protease K (20mg/ml, 3115879 BMB) and further de-crosslinked at 65℃ for 2h. De-crosslinked DNA was added with 10ml 3M sodium acetate pH 5.2 and purified with QIAquick PCR Purification kit (QIAGEN 28106) according to manufacture instruction.
Library construction was performed using Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012) according to manufacturer’s specifications with the addition of size selection (left side at 0.9x, right side at 0.6x) using SPRIselect beads (Beckman Coulter, catalog no. B23318) prior to PCR amplification. Library size was determined (average 351 bp, range 333-372 bp) using the Agilent Bioanalyzer 2100, followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Libraries were then pooled and sequenced on the Illumina NextSeq 500 platform using Illumina sequencing reagents according to manufacturer’s instructions

treatment_protocol: Cells were synchronized to pro-metaphase with 200ng/ml nocodazole for 7-8.5h. For post-mitotic enrichment, cells were released from nocodazole for 0, 25min, 60min, 120min and 240min for pro-meta, ana/telo, early-G1, mid-G1 and late-G1 respectively.

tag: cell type

value: erythroid


title: RGC061616p10_B4_S304


title: ChIP-seq-PolII-early-g1-rep1


title: ChIP-seq-PolII-anatelo-rep2


title: ChIP-seq-PolII-mid-g1-rep1


title: ChIP-seq-PolII-mid-g1-rep2


title: ChIP-seq-PolII-early-g1-rep2


title: ChIP-seq-PolII-anatelo-rep3


title: ChIP-seq-PolII-early-g1-rep3


title: ChIP-seq-PolII-late-g1-rep3


title: ChIP-seq-PolII-prometa-rep2


title: ChIP-seq-PolII-late-g1-rep2


title: ChIP-seq-PolII-prometa-rep1


title: Capture-C-commd3_mutant_mid-G1-rep2

data_processing:
Library strategy: Capture-C
Raw read quality were assessed with Trim Galore (a wrapper for FastQC and Cutadapt). Trimmed reads were merged or interleaved using FLASH 1.2.8. Concatenated reads were then in silico digested with DpnII, aligned to mm9 and analyzed using CCAnalyzer3. Interactions were normalized to total interactions to generate bedgraph files for each bait/condition. Bedgraph files from each individual replicate was merged.
Genome_build: mm9

extract_protocol:
Capture-C experiments were performed as previously described (Hughes et al. Nat. Genet. 2014, Huang et al. Genes Dev. 2017). 3C library preparation was similar to that of in-situ HiC experiments without biotin nucleotide labeling. Briefly, cells were fixed with 1% PFA and sorted at designated cell cycle stages. DNA was directly ligated after DpnII digestion, extracted with pheno-chloroform and fragmented.
Ligated DNA was purified, fragmented and converted into 3C library using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040, M0543L, E7335S). After indexation with NEBNext multiplex oligos, DNA was cleaned up with AMPure XP beads and further amplified with Illumina P5 and P7 primers for 6 cycles. To perform oligo pull-down, 3C libraries were completely dried on a thermal cycler at 60℃. Dried DNA was re-constituted with 13ul hybridization mixture (2.5ul nuclease free water, 7.5ul 2xhybridization buffer, 3ul hybridization component A, Nimblegen SeqCap Hybridization and Wash kit) for 10min at room temperature. DNA was denatured at 95℃ for 10min and then added with 2ul 3pmole biotin-labeled capture probe pool to make a 15ul hybridization system. Hybridization was immediately carried out at 47℃ for more than 24h on a thermal cycler. Hybridized DNA was pulled down with Dynabeads MyOne Streptavidin C1 beads (40ul per capture) and washed with Nimblegen SeqCap Hybridization and Wash kit according to manufacture instruction. Captured DNA was then eluted into 25ul 0.125N NaOH, followed by HCl neutralization. Captured DNA was then purified with AMPure XP beads. Purified DNA was then amplified with Illumina P5 and P7 primer for 12 cycles and PCR products were cleaned up with AMPure XP beads. PCR products were dried on a thermal cycler at 60℃ to initiate a similar second round of capture for further enrichment of targeted DNA. DNA was eluted into 25ul nuclease-free water and subject to sequencing with Illumina NextSeq 500 platform using Illumina sequencing reagents according to manufacturer’s instructions.


title: Capture-C-commd3_mutant_ana.telo-rep2


title: Capture-C-commd3_mutant_prometa-rep2


title: Capture-C-commd3_mutant_mid-G1-rep1


title: ChIP-seq-PolII-mid-g1-rep3


title: Capture-C-commd3_mutant_early-G1-rep2


title: Capture-C-commd3_mutant_prometa-rep1


title: Capture-C-commd3_mutant_ana.telo-rep1


title: Capture-C-commd3_mutant_early-G1-rep1


title: ChIP-seq-input-ana.telo

description: ChIP-seq


title: ChIP-seq-input-early-G1

description: ChIP-seq


title: ChIP-seq-input-prometa

description: ChIP-seq


title: ChIP-seq-input-asyn

description: ChIP-seq


title: ChIP-seq-PolII-anatelo-rep1


title: ChIP-seq-input-mid-G1

description: ChIP-seq


title: ChIP-seq-Rad21-late-G1-rep1

description: ChIP-seq


title: ChIP-seq-Rad21-mid-G1-rep1

description: ChIP-seq


title: ChIP-seq-Rad21-mid-G1-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-early-G1-rep1

description: ChIP-seq


title: ChIP-seq-Rad21-late-G1-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-asyn-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-ana.telo-rep2

description: ChIP-seq


title: ChIP-seq-input-late-G1

description: ChIP-seq


title: ChIP-seq-CTCF-late-G1-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-early-G1-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-ana.telo-rep1

description: ChIP-seq


title: ChIP-seq-Rad21-prometa-rep2

description: ChIP-seq


title: ChIP-seq-Rad21-asyn-rep1

description: ChIP-seq


title: ChIP-seq-CTCF-early-G1-rep1

description: ChIP-seq


title: ChIP-seq-CTCF-prometa-rep2

description: ChIP-seq


title: ChIP-seq-CTCF-prometa-rep3

description: ChIP-seq


title: ChIP-seq-CTCF-ana.telo-rep1

description: ChIP-seq


title: ChIP-seq-CTCF-early-G1-rep2

description: ChIP-seq


title: ChIP-seq-CTCF-ana.telo-rep2

description: ChIP-seq


title: ChIP-seq-CTCF-mid-G1-rep1

description: ChIP-seq


title: ChIP-seq-CTCF-asyn-rep2

description: ChIP-seq


title: ChIP-seq-CTCF-asyn-rep1

description: ChIP-seq


title: ChIP-seq-CTCF-prometa-rep1

description: ChIP-seq


title: ChIP-seq-Rad21-prometa-rep1

description: ChIP-seq